From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 25 Sep 2013 01:08:23 +0000 (+0000)
Subject: inprogress
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f8073a938000c51355cea72079dea419bdecd070;p=jalview.git

inprogress
---

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 087f8e1..e68b220 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -161,24 +161,25 @@ public final class Configuration {
     final static String                     display_options[][]                                    = {
             { "Phylogram", "display", "?" }, { "Node Name", "display", "yes" }, { "Taxonomy Code", "display", "yes" },
             { "Seq Annotations", "nodisplay", "no" }, { "Confidence Values", "display", "?" },
-            { "Node Events", "display", "?" }, { "Taxonomy Colorize", "display", "yes" },
-            { "Colorize Branches", "display", "no" }, { "Use Branch-Widths", "display", "no" },
-            { "Show Custom Nodes", "display", "yes" }, { "Domains", "nodisplay", "no" },
+            { "Node Events", "display", "?" }, { "Colorize by Taxonomy", "display", "yes" },
+            { "Use Branch Colors", "display", "no" }, { "Use Branch Widths", "display", "no" },
+            { "Show Custom Nodes", "display", "yes" }, { "Protein Domains", "nodisplay", "no" },
             { "Binary Characters", "nodisplay", "no" }, { "Binary Char Counts", "nodisplay", "no" },
             { "Seq Name", "display", "yes" }, { "Seq Acc", "display", "no" },
             { "Show Internal Data", "display", "yes" }, { "Dyna Hide", "display", "yes" },
             { "Taxonomy Scientific", "display", "yes" }, { "Taxonomy Common", "display", "no" },
-            { "Annotation Colorize", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
+            { "Colorize by Annotation", "nodisplay", "no" }, { "Seq Symbol", "display", "yes" },
             { "Rollover", "display", "yes" }, { "Relation Confidence", "nodisplay", "no" },
             { "Vector Data", "nodisplay", "no" }, { "Taxonomy Images", "display", "no" },
             { "Properties", "nodisplay", "no" }                                                   };
     final static String                     clickto_options[][]                                    = {
             { "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
-            { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
-            { "Open Sequence Web", "display" }, { "Open Taxonomy Web", "display" }, { "Blast", "display" },
-            { "Cut Subtree", "display" }, { "Copy Subtree", "display" }, { "Paste Subtree", "display" },
-            { "Delete Subtree/Node", "display" }, { "Add New Node", "display" }, { "Edit Node Data", "display" },
-            { "Sort Descendants", "display" }, { "Return", "display" }, { "Select Node(s)", "display" } };
+            { "Sub/Super Tree", "display" }, { "Swap Descendants", "display" },
+            { "Colorize Subtree/Node(s)", "display" }, { "Open Sequence DB", "display" },
+            { "Open Taxonomy DB", "display" }, { "Blast", "display" }, { "Cut Subtree", "display" },
+            { "Copy Subtree", "display" }, { "Paste Subtree", "display" }, { "Delete Subtree/Node", "display" },
+            { "Add New Node", "display" }, { "Edit Node Data", "display" }, { "Sort Descendants", "display" },
+            { "Return", "display" }, { "Select Node(s)", "display" }                              };
     // This option is selected in the dropdown
     int                                     default_clickto                                        = Configuration.display_node_data;
     // --------------
diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 6df3e33..eab1ea8 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -1728,6 +1728,14 @@ final class ControlPanel extends JPanel implements ActionListener {
             }
             cb_index++;
         }
+        if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
+            _select_nodes_item = cb_index;
+            addClickToOption( Configuration.select_nodes, _configuration.getClickToTitle( Configuration.select_nodes ) );
+            if ( default_option == Configuration.select_nodes ) {
+                selected_index = cb_index;
+            }
+            cb_index++;
+        }
         if ( _configuration.doDisplayClickToOption( Configuration.get_ext_desc_data ) ) {
             _get_ext_desc_data = cb_index;
             if ( !ForesterUtil.isEmpty( getConfiguration().getLabelForGetExtDescendentsData() ) ) {
@@ -1830,15 +1838,6 @@ final class ControlPanel extends JPanel implements ActionListener {
                 }
                 cb_index++;
             }
-            if ( _configuration.doDisplayClickToOption( Configuration.select_nodes ) ) {
-                _select_nodes_item = cb_index;
-                addClickToOption( Configuration.select_nodes,
-                                  _configuration.getClickToTitle( Configuration.select_nodes ) );
-                if ( default_option == Configuration.select_nodes ) {
-                    selected_index = cb_index;
-                }
-                cb_index++;
-            }
         }
         // Set default selection and its action
         _click_to_combobox.setSelectedIndex( selected_index );